Dissolved silicon (dSi) is a key nutrient in the oceans, but data regarding Si isotopes in coastal aquifers are not widely available. Here we investigate the Si isotopic composition of 12 fresh and 16 saline groundwater samples from Rottnest Island, Western Australia, which forms part of the world's most extensive aeolianite deposit (the Tamala Limestone formation). In total, two bedrock samples were also collected from Rottnest Island for Si isotope analysis. The δ30Si values of groundwater samples ranged from −0.4 ‰ to +3.6 ‰ with an average +1.6 ‰, and the rock samples were −0.8 ‰ and −0.1 ‰. The increase in δ30Si values in fresh groundwater is attributed to the removal of the lighter Si isotopes into secondary minerals and potentially also adsorption onto Fe (oxy)hydroxides. The positive correlations between δ30Si values and dSi concentrations (ρ = 0.59; p = 0.02) and δ30Si values and Cl, but not dSi and Cl concentrations, are consistent with vertical mixing between the younger fresh groundwater and the deeper groundwater, which have undergone a greater degree of water–rock interactions. This has produced a spatial pattern in δ30Si across the aquifer due to the local hydrogeology, resulting in a correlation between δ30Si and tritium activities when considering all groundwater types (ρ = −0.68; p = 0.0002). In the deeper aquifer, the inverse correlation between dSi and Cl concentrations (ρ = −0.79; p = 0.04) for the more saline groundwater is attributed to groundwater mixing with local seawater that is depleted in dSi (< 3.6 µM). Our results from this well-constrained island aquifer system demonstrate that stable Si isotopes usefully reflect the degree of water–aquifer interactions, which is related to groundwater residence time and local hydrogeology. Our finding that lithogenic Si dissolution occurs in the freshwater lens and the freshwater–seawater transition zone on Rottnest Island appears to supports the recent inclusion of a marine–submarine groundwater discharge term in the global dSi mass balance. Geologically young carbonate aquifers, such as Rottnest Island, may be an important source of dSi in coastal regions with low riverine input and low oceanic dSi concentrations.